WASHINGTON — The backroom battling over this week’s government funding bill had one key casualty — a clause granting federal agencies such as the Defense Department greater flexibility to cope with forced spending cuts known as sequestration.

The controversial cuts began in March under a provision of the 2011 Budget Control Act, and have roiled the federal government ever since. The Pentagon has been especially frustrated by the spending cuts, which are scheduled to take effect again in January and hold the base DOD budget to $475 billion — some $50 billion below President Barack Obama’s 2014 budget proposal. Congress’ vote this week to reopen the government essentially continued sequestration along with current spending levels.

Pentagon officials say the arbitrary, across-the-board nature of the cuts makes it difficult to comply because of the complexity and systematic nature of DOD spending, and have testified before congressional panels that they need flexibility.

Under the newly passed resolution, defense leaders have no ability to use money for higher priority purposes — like operations and maintenance — rather than on purchases that could be delayed, DOD Comptroller Robert F. Hale said Thursday at the Pentagon.

Hale said his office has had discussions with leaders from the various military services about reining in spending early in the fiscal year to prepare for sequestration.

“We have very little flexibility under the continuing resolution,” Hale said. “We can’t move between those accounts at all, and generally, we aren’t allowed to reprogram when we’re under continuing resolution, so for a while we kind of have to hold our breath and try to look to the future and be as conservative as we can.”

During this week’s negotiations over reopening the federal government and raising the debt ceiling, Senate GOP Leader Mitch McConnell of Kentucky was pushing for a provision that would have done just that — give agencies such as DOD greater flexibility to make sequestration cuts.

McConnell didn’t get his wish. His spokesman, Don Stewart, said the flexibility provision was in the original shutdown/debt ceiling bill drafted two weeks ago by GOP Sen. Susan Collins of Maine.

“It’s good policy, and we tried to include it,” Stewart said. “We’ll keep trying. It’s not going away.”

“Sen. Levin is still hoping to get rid of sequestration altogether,” Long said, “by replacing it with a balanced package of targeted cuts, entitlement reforms, and revenue increases.”

Even without the provision, McConnell took to the Senate floor Wednesday to praise sequestration as a critical law that Republicans will insist continue during long-term budget negotiations that will begin later this fall.

“That’s been a top priority for me and my Republican colleagues throughout this debate. And it’s been worth the effort,” McConnell said. “We’re not going back on this agreement.

“Let’s not understate the importance of the BCA, or the importance of the fight to preserve it. This legislation is the largest spending reduction bill of the last quarter-century, and the largest deficit reduction bill since 1981 that didn’t include a tax hike. Preserving this law is critically important.”

In the 2013 fiscal year, sequestration cut $37 billion from both the Pentagon’s base budget and wartime budget, forcing civilian furloughs, the cancellation of many types of training operations, deferred maintenance and even canceled ship deployments.

If it continues in 2014 and beyond, Defense officials say cuts could cause major cuts in ground forces, civilians layoffs, the decommissioning of aircraft carriers and elimination of air wings.

Former Defense Secretary Leon Panetta, in Washington this week, said congressional leaders designed sequestration to be “crazy,” and agreed that the forced cuts have created “havoc” at the Defense Department.

But, leaning on his past as a House Budget Committee chairman and Office of Management and Budget director, Panetta said a flexibility provision wouldn’t have solved the underlying problem.

“Instead of playing with ideas as to how you create flexibility to move money around within the bounds of sequestration, I would rather [Congress] deal with the bigger issues of the budget and be able to de-trigger sequestration,” he said. “That would be the more responsible approach.”

When pressed on whether more flexibility would at least help DOD, Panetta replied that DOD “is already drowning in quicksand … They’ll take whatever rope you throw them.”

Appearing Sept. 15 before the House Armed Services Committee, leaders of the Army, Air Force, Marines and Navy warned that continuing sequestration would dangerously jeopardize the ability of all four services to stay capable and ready for action.

“There should be no misunderstanding: Cuts of this magnitude will have a significant impact on the global security climate, the perceptions of our enemies and the confidence of our allies,” Marine Corps Commandant Gen. James Amos told the committee.

“The abruptness and inflexibility of sequestration will force us to mortgage the condition of our equipment and could erode our readiness to dangerous levels. The indiscriminate nature of sequestration is creating its very own national security problem.”